AMBER Archive (2007)

Subject: AMBER: problem with distance restraints

From: Ed Pate (pate_at_math.wsu.edu)
Date: Mon Jan 22 2007 - 13:43:58 CST

Dear Amber community:

I am attempting to run a GB simulation with NMR distance restraints
between two pairs of atoms and additional restraints on another group of
atoms. For my template, I have tried to use the Amber tutorial .AMBER
Refinement of a DNA Duplex. and the advice for combining the two types of
restraint in http://amber.scripps.edu/Questions/mail/8.html.

I am using Amber8 compiled with Portland group compilers. Prior to adding
the nmr restraints, I was able to get the job to run successfully with
just the other restraints.

The job now terminates with the following error message:
Warning: Error opening "Old" file from subroutine OPNMRG
  File = DIST

My md.in and DISANG files are appended.

I would appreciate it if anyone sees what I am doing wrong.

Thanks,

Ed Pate

My md.in file follows:
&cntrl
   ntc=2,
   ntf=2,
   cut=20.0,
   igb=2,
   saltcon=0.2,
   gbsa=1,
   ntpr=5,
   nstlim=100,
   dt=0.002,
   ntt=1,
   tempi=300.0,
   temp0=300.,
   tautp=2.0,
   ntx=1,
   irest=0,
   ntb=0,
   ntwx=2500,
   ntwr=1000
   nscm=1000,
   nrespa=2,
   ntr=1,
   nmropt=1,
  &end
  &wt
   type='END',
  &end
LISTOUT=POUT
DISANG=DIST
   restrain the following
   1.0
RES 1 1
RES 3 7
RES 18 43
RES 45 85
RES 91 100
END
END

My DISANG file follows:

&rst
   ixpk=0, nxpk =0, iat=11899, 1825, r1= 6.6,r2=7.6,r3=8.3,r4=8.8,
      rk2=0. rk3=32.,irg6=1, ialtd=0,
  &end
  &rst
   ixpk=0, nxpk=0, iat=11926, 2911, r1=3.76 , r2=4.76, r3=5.46, r4=5.96,
      rk2=0., rk3=32., irg6=1, ialtd=0,
  &end

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